written cutadapt task

cutadapt.wdl

 task cutadapt {
+    File read1
+    File? read2
+    String read1output
+    String? read2output
     String? format
+    String? condaEnv
     Int? cores = 1
-    String? adapter3end
-    String? adapter5end
-    String? adapterAnywhere
+    Array[String]? adapter
+    Array[String]? front
+    Array[String]? anywhere
+    Array[String]? adapterRead2
+    Array[String]? frontRead2
+    Array[String]? anywhereRead2
+    Boolean? interleaved
+    String? pairFilter
     Float? errorRate
     Boolean? noIndels
-    Int? count
-    Int? minLength
+    Int? times
+    Int? overlap
     Boolean? matchReadWildcards
     Boolean? noMatchAdapterWildcards
     Boolean? noTrim
-    String? maskAdapter
-    Int? cutLength
+    Boolean? maskAdapter
+    Int? cut
+    String? nextseqTrim
+    String? qualityCutoff
+    Int? qualityBase
+    Int? length
+    Boolean? trimN
+    String? lengthTag
+    String? stripSuffix
+    String? prefix
+    String? suffix
+    Int? minimumLength
+    Int? maximumLength
+    Int? maxN
+    Boolean? discardTrimmed
+    Boolean? discardUntrimmed
+    String? infoFilePath
+    String? restFilePath
+    String? wildcardFilePath
+    String? tooShortOutputPath
+    String? tooLongOutputPath
+    String? untrimmedOutputPath
+    String? tooShortPairedOutputPath
+    String? tooLongPairedOutputPath
+    String? untrimmedPairedOutputPath
+    Boolean? colorspace
+    Boolean? doubleEncode
+    Boolean? trimPrimer
+    Boolean? stripF3
+    Boolean? maq
+    Boolean? bwa
+    Boolean? zeroCap
+    Boolean? noZeroCap
 
+    command {
+        set -e -o pipefail
+        ${"source activate " + condaEnv}
+        cutadapt \
+        ${"--cores=" + cores} \
+        ${sep="-a " "-a " + adapter} ${"-A " + adapterRead2} \
+        ${"-g" + front} ${"-G" + frontRead2} \
+        ${"-b " + anywhere} ${"-B" + anywhereRead2} \
+        --output ${read1output} ${"--paired-output " + read2output} \
+        ${"--to-short-output " + tooShortOutputPath} ${"--to-short-paired-output " + tooShortPairedOutputPath} \
+        ${"--to-long-output " + tooLongOutputPath} ${"--to-long-paired-output " + tooLongPairedOutputPath} \
+        ${"--untrimmed-output " + untrimmedOutputPath} ${"--untrimmed-paired-output " + untrimmedPairedOutputPath} \
+        ${"--pair-filter " + pairFilter} \
+        ${"--error-rate " + errorRate} \
+        ${"--times " + times} \
+        ${"--overlap " + overlap} \
+        ${"--cut " + cut} \
+        ${"--nextseq-trim " + nextseqTrim} \
+        ${"--quality-cutoff " + qualityCutoff} \
+        ${"--quality-base " + qualityBase} \
+        ${"--length " + length} \
+        ${"--length-tag " + lengthTag} \
+        ${"--strip-suffix " + stripSuffix} \
+        ${"--prefix " + prefix} \
+        ${"--suffix " + suffix} \
+        ${"--minimum-length " + minimumLength} \
+        ${"--maximum-length " + maximumLength} \
+        ${"--max-n " + maxN} \
+        ${true="--discard-untrimmed" false="" discardUntrimmed} \
+        ${"--info-file " + infoFilePath } \
+        ${"--rest-file " + restFilePath } \
+        ${"--wildcard-file " + wildcardFilePath} \
+        ${true="--match-read-wildcards" false="" matchReadWildcards} ${true="--no-match-adapter-wildcards" false="" noMatchAdapterWildcards} \
+        ${true="--no-trim" false="" noTrim} ${true="--mask-adapter" false="" maskAdapter} \
+        ${true="--no-indels" false="" noIndels} ${true="--trim-n" false="" trimN}  \
+        ${true="--interleaved" false="" interleaved} ${true="--discard-trimmed" false="" discardTrimmed } \
+        ${true="--colorspace" false="" colorspace} ${true="--double-encode" false="" doubleEncode} \
+        ${true="--strip-f3" false="" stripF3} ${true="--maq" false="" maq} ${true="--bwa" false="" bwa} \
+        ${true="--zero-cap" false="" zeroCap} ${true="--no-zero-cap" false="" noZeroCap} \
+        ${read1} ${read2}
+    }
+    output{
+        File report = file(stdout())
+        File cutRead1 = read1output
+        File? cutRead2 = read2output
+        File? tooLongOutput=tooLongOutputPath
+        File? tooShortOutput=tooShortOutputPath
+        File? untrimmedOutput=untrimmedOutputPath
+        File? tooLongPairedOutput=tooLongPairedOutputPath
+        File? tooShortPairedOutput=tooShortPairedOutputPath
+        File? untrimmedPairedOutput=untrimmedPairedOutputPath
+        File? infoFile=infoFilePath
+        File? restFile=restFilePath
+        File? wildcardFile=wildcardFilePath
+    }
+    runtime {
+        cpu: select_first(cores)
+    }
 }
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